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3tca

Crystal structure of the Ras-associating and pleckstrin-homology domains of RIAM

Method: X-RAY DIFFRACTION Dmax: 85.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Amyloid beta A4 precursor protein-binding family B member 1-interacting protein

Mus musculus

UniProt Q8R5A3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 150–437 Fragment：Ras-associating and PH domain, UNP residues 150-437 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；298 K；12% PEG3350, 100 mM LiAc, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.35 Å R-free 0.282
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 150–437 Fragment：Ras-associating and PH domain, UNP residues 150-437 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；298 K；12% PEG3350, 100 mM LiAc, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.35 Å R-free 0.282

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3TCA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4KVG Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1 Deposited 2013-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 179–437（259 aa） Fragment：RA-PH domains (UNP residues 179-437)
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M ammonium sulfate, 0.1M Tris, 15% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.65 Å R-free 0.219
4KVG Crystal structure of RIAM RA-PH domains in complex with GTP bound Rap1 Deposited 2013-05-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 179–437（259 aa） Fragment：RA-PH domains (UNP residues 179-437)
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M ammonium sulfate, 0.1M Tris, 15% PEG 1500, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.65 Å R-free 0.219
4W8P Crystal structure of RIAM TBS1 in complex with talin R7R8 domains Deposited 2014-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–25（21 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM NaCl, 20% (w/v) polyethylene glycol 3350 and 20% (v/v) ethylene glycol
Resolution 1.50 Å R-free 0.242
4W8P Crystal structure of RIAM TBS1 in complex with talin R7R8 domains Deposited 2014-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 5–25（21 aa）
Not recorded EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100 mM NaCl, 20% (w/v) polyethylene glycol 3350 and 20% (v/v) ethylene glycol
Resolution 1.50 Å R-free 0.242
6O6H RIAM cc-RA-PH structure in the P21212 space group Deposited 2019-03-06 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 150–437（288 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM sodium malonate pH 6.0, 16% PEG 3350, 3% 1,4-dioxane
Resolution 2.50 Å R-free 0.281
6OLU RIAM RA-PH core structure in the P212121 space group Deposited 2019-04-17 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 179–437（259 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；8% v/v Tacsimate pH 6, 20% w/v PEG3350
Resolution 1.90 Å R-free 0.256

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AB1IP_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–291； UniProt 150–437 Author chain B； PDBConstruct 4–291； UniProt 150–437

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3tca

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3tca
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3tca
Deposition date deposition_date2011-08-08
Structure title titleCrystal structure of the Ras-associating and pleckstrin-homology domains of RIAM
Keywords keywordsRA DOMAIN, RBD, PH DOMAIN, RAP1-INTERACTING ADAPTOR MOLECULE, INTEGRIN SIGNALING, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier26.39 Å
Radius of gyration Rg (electron density) rg_electron25.10 Å
Forward intensity I(0) i052298800.00
Molecular weight molecular_weight56791.0 kDa
Excluded volume excluded_volume71311 ų
Envelope volume envelope_volume88988 ų
Hydration-shell volume shell_volume29689 ų
Envelope diameter envelope_diameter90.0 Å
Shell Rg shell_rg32.24 Å
Envelope Rg envelope_rg24.94 Å
Shape Rg shape_rg25.06 Å
Total Rg total_rg26.05 Å
Total atoms total_atoms3995
Residues n_residues491
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax85.1 Å
Rg (real space) rg_real26.34 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real5.2300e+07
I(0) uncertainty (real space) i0_real_error7.6390e+05
Rg (reciprocal space) rg_reciprocal26.36 Å
I(0) (reciprocal space) i0_reciprocal52300000.0000
Solution quality estimate total_estimate0.8964
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary83.7 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.326
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9793000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.967
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3tcaA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3tcaA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
Domain ID domain_id3tcaB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id3tcaB02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)